Both average hemispheres look very bad, they don't even look like a brain. The two monkey surfaces look reasonable, except for some topological defect that I think could be fixed with some manual editing. Is there anything I could try?

Thanks a lot Francesca

2018-03-14 23:41 GMT+01:00 Douglas N. Greve dgreve@mgh.harvard.edu:

I don't know what is going on there except that the average surfaces are probably wrong in some way. It looks like it made it all the way through except for that step, so all of the output should be there. How does it look?

On 03/13/2018 05:27 PM, Francesca Strappini wrote:

...

Dear Experts,

I'm trying to average two monkey brains. I run this command line:

make_average_subject --subjects MonkeyCelia MonkeyCassis --out

AVGmonkeys

...

but it ended with errors.

I run the recon-all for both monkyes with the option -notal-check because I had problems with the Talairach registration. I don't know if this could be the cause.

Thanks a lot Francesca

Tue Mar 13 20:04:06 CET 2018 /usr/local/freesurfer/subjects/AVGmonkeys /usr/local/freesurfer/bin/recon-all -s AVGmonkeys -cortribbon -aparc2aseg subjid AVGmonkeys setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_

64-stable-pub-v6.0.0-2beb96c

...

Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63682 maxlocks unlimited maxsignal 63682 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited

          total        used        free      shared buff/cache

available Mem: 16350220 4943572 7520800 278988 3885848 10739864 Swap: 19528700 0 19528700

######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Cortical ribbon mask Tue Mar 13 20:04:06 CET 2018 /usr/local/freesurfer/subjects/AVGmonkeys/mri

mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon AVGmonkeys

SUBJECTS_DIR is /usr/local/freesurfer/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 34535 writing volume /usr/local/freesurfer/subjects/AVGmonkeys/mri/ribbon.mgz ERROR: ribbon has non-zero value at location 0,0,0 Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s AVGmonkeys exited with ERRORS at Tue Mar 13 20:26:58 CET

2018

...

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il mailto:francesca.strappini@weizmann.ac.il

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Thank you, Doug! One monkey has a pretty decent registration while the other one does not even appear in the window when I try to manually check the registration with this command line: tkregister --mgz --s MonkeyCelia --fstal --surf orig It looks like if there is no brain.

2018-03-15 16:57 GMT+01:00 Douglas N. Greve dgreve@mgh.harvard.edu:

Check the talairach.xfm registration. It is probably way off. It does not have to be perfect (esp since they are different species), but the two subjects should have a similar registration

On 03/14/2018 07:27 PM, Francesca Strappini wrote:

...

Both average hemispheres look very bad, they don't even look like a brain. The two monkey surfaces look reasonable, except for some topological defect that I think could be fixed with some manual editing. Is there anything I could try?

Thanks a lot Francesca

2018-03-14 23:41 GMT+01:00 Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:

I don't know what is going on there except that the average
surfaces are
probably wrong in some way. It looks like it made it all the way
through
except for that step, so all of the output should be there. How
does it
look?


On 03/13/2018 05:27 PM, Francesca Strappini wrote:
> Dear Experts,
>
> I'm trying to average two monkey brains. I run this command line:
>
>  make_average_subject --subjects MonkeyCelia MonkeyCassis --out
AVGmonkeys
>
> but it ended with errors.
>
> I run the recon-all for both monkyes with the option -notal-check
> because I had problems with the Talairach registration. I don't

know

...

> if this could be the cause.
>
> Thanks a lot
> Francesca
>
> Tue Mar 13 20:04:06 CET 2018
> /usr/local/freesurfer/subjects/AVGmonkeys
> /usr/local/freesurfer/bin/recon-all
> -s AVGmonkeys -cortribbon -aparc2aseg
> subjid AVGmonkeys
> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
> FREESURFER_HOME /usr/local/freesurfer
> Actual FREESURFER_HOME /usr/local/freesurfer
> build-stamp.txt:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12

21:23:04

...

> UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> cputime      unlimited
> filesize     unlimited
> datasize     unlimited
> stacksize    8192 kbytes
> coredumpsize 0 kbytes
> memoryuse    unlimited
> vmemoryuse   unlimited
> descriptors  1024
> memorylocked 64 kbytes
> maxproc      63682
> maxlocks     unlimited
> maxsignal    63682
> maxmessage   819200
> maxnice      0
> maxrtprio    0
> maxrttime    unlimited
>
>               total        used        free shared buff/cache
> available
> Mem:       16350220     4943572     7520800 278988 3885848
> 10739864
> Swap:      19528700           0    19528700
>
> ########################################
> program versions used
> $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
> $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman
Exp $
> mri_convert.bin -all-info
> ProgramName: mri_convert.bin  ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v
1.226
> 2016/02/26 16:15:24 mreuter Exp $  User: francesca Machine:

shalimpc

...

> Platform: Linux  PlatformVersion: 4.4.0-116-generic
CompilerName: GCC
> CompilerVersion: 40400
> FLIRT version 5.5
> $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
> mri_convert.bin --version
> stable6
> ProgramName: tkregister2_cmdl  ProgramArguments: --all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v
> 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: francesca

Machine:

...

> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> Program nu_correct, built from:
> Package MNI N3, version 1.12.0, compiled by nicks@terrier
> (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
> ProgramName: mri_make_uchar  ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_make_uchar.c,v 1.4
> 2011/03/02 00:04:14 nicks Exp $  User: francesca Machine: shalimpc
> Platform: Linux  PlatformVersion: 4.4.0-116-generic
CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mri_normalize  ProgramArguments: -all-info
> ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v
> 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: francesca
Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_watershed  ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v
> 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: francesca  Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_gcut  ProgramArguments: -all-info ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02
> 00:04:16 nicks Exp $  User: francesca  Machine: shalimpc  Platform:
> Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mri_segment  ProgramArguments: -all-info
ProgramVersion:
> $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan

18

...

> 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27
22:24:52
> zkaufman Exp $  User: francesca  Machine: shalimpc Platform: Linux
> PlatformVersion: 4.4.0-116-generic CompilerName: GCC
CompilerVersion:
> 40400
> ProgramName: mri_label2label.bin  ProgramArguments: -all-info
> ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v
> 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: francesca
Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_em_register  ProgramArguments: -all-info
> ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v
> 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User: francesca
> Machine: shalimpc Platform: Linux  PlatformVersion:
4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_ca_normalize  ProgramArguments: -all-info
> ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:

mri_ca_normalize.c,v

...

> 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $  User: francesca
Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_ca_register  ProgramArguments: -all-info
> ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_register.c,v
> 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $  User: francesca
Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_ca_label  ProgramArguments: -all-info
ProgramVersion:
> $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan

18

...

> 2017 16:38:58  CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27
> 22:25:10 zkaufman Exp $  User: francesca  Machine: shalimpc
Platform:
> Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mri_pretess  ProgramArguments: -all-info
ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mri_pretess.c,v 1.22 2013/08/30
> 18:12:25 mreuter Exp $  User: francesca  Machine: shalimpc
Platform:
> Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mri_fill  ProgramArguments: -all-info ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mri_fill.c,v 1.119 2011/10/25
14:09:58
> fischl Exp $  User: francesca  Machine: shalimpc Platform: Linux
> PlatformVersion: 4.4.0-116-generic  CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mri_tessellate  ProgramArguments: -all-info
> ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_tessellate.c,v
> 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $  User: francesca
Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
> mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $  User:
> francesca  Machine: shalimpc Platform: Linux PlatformVersion:
> 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400
> ProgramName: mri_normalize_tp2  ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_normalize_tp2.c,v
> 1.8 2011/03/02 00:04:23 nicks Exp $  User: francesca  Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mris_smooth  ProgramArguments: -all-info
ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30 2014/01/21
> 18:48:21 fischl Exp $  User: francesca  Machine: shalimpc

Platform:

...

> Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mris_inflate  ProgramArguments: -all-info
ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45 2016/01/20
> 23:42:15 greve Exp $  User: francesca  Machine: shalimpc Platform:
> Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mris_curvature  ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature.c,v
> 1.31 2011/03/02 00:04:30 nicks Exp $  User: francesca  Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mris_sphere  ProgramArguments: -all-info
ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mris_sphere.c,v 1.61 2016/01/20
> 23:42:15 greve Exp $  User: francesca  Machine: shalimpc  Platform:
> Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mris_fix_topology  ProgramArguments: -all-info
> ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mris_fix_topology.c,v
> 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $  User: francesca
Machine:
> shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mris_topo_fixer  ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mris_topo_fixer.cpp,v
> 1.29 2011/03/02 00:04:34 nicks Exp $  User: francesca  Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mris_ca_label  ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mris_ca_label.c,v 1.37
> 2014/02/04 17:46:42 fischl Exp $  User: francesca Machine: shalimpc
> Platform: Linux  PlatformVersion: 4.4.0-116-generic
CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mris_euler_number  ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mris_euler_number.c,v
> 1.10 2013/01/14 22:39:14 greve Exp $  User: francesca  Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mris_make_surfaces  ProgramArguments: -all-info
> ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mris_make_surfaces.c,v
> 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $  User: francesca
Machine:
> shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mris_register  ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mris_register.c,v 1.63
> 2016/01/20 23:43:04 greve Exp $  User: francesca Machine: shalimpc
> Platform: Linux  PlatformVersion: 4.4.0-116-generic
CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mris_volmask  ProgramArguments: --all-info
> ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_volmask.cpp,v
> 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $  User: francesca
Machine:
> shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
> CompilerName: GCC  CompilerVersion: 40400
> ProgramName: mris_anatomical_stats ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
> mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $
User:
> francesca  Machine: shalimpc  Platform: Linux PlatformVersion:
> 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
> ProgramName: mrisp_paint  ProgramArguments: -all-info
ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22
> 14:47:57 fischl Exp $  User: francesca  Machine: shalimpc

Platform:

...

> Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mris_curvature_stats ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
> mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $

User:

...

> francesca  Machine: shalimpc Platform: Linux PlatformVersion:
> 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400
> ProgramName: mris_calc  ProgramArguments: -all-info ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27
> 18:51:28 greve Exp $  User: francesca  Machine: shalimpc Platform:
> Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
> CompilerVersion: 40400
> $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
>
> ProgramName: mri_robust_register.bin ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
> mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
User:
> francesca  Machine: shalimpc  Platform: Linux PlatformVersion:
> 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
> $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter
Exp $
>
> ProgramName: mri_robust_template  ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
> mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
> User: francesca  Machine: shalimpc  Platform: Linux
PlatformVersion:
> 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
> ProgramName: mri_and  ProgramArguments: -all-info ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13
> nicks Exp $  User: francesca  Machine: shalimpc Platform: Linux
> PlatformVersion: 4.4.0-116-generic  CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mri_or  ProgramArguments: -all-info ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29
> lzollei Exp $  User: francesca  Machine: shalimpc Platform: Linux
> PlatformVersion: 4.4.0-116-generic  CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mri_fuse_segmentations ProgramArguments: -all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
> mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $
User:
> francesca  Machine: shalimpc  Platform: Linux PlatformVersion:
> 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
> ProgramName: mri_segstats  ProgramArguments: -all-info
ProgramVersion:
> $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp:
> Jan 18 2017 16:38:58  CVS: $Id: mri_segstats.c,v 1.121 2016/05/31
> 17:27:11 greve Exp $  User: francesca  Machine: shalimpc Platform:
> Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
> CompilerVersion: 40400
> ProgramName: mri_relabel_hypointensities ProgramArguments:
-all-info
> ProgramVersion: $Name: stable6 $  TimeStamp:
2018/03/13-19:04:06-GMT
> BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
> mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks
Exp $
> User: francesca  Machine: shalimpc  Platform: Linux
PlatformVersion:
> 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
> #######################################
> GCADIR /usr/local/freesurfer/average
> GCA RB_all_2016-05-10.vc700.gca
> GCASkull RB_all_withskull_2016-05-10.vc700.gca
> AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
> GCSDIR /usr/local/freesurfer/average
> GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
> #######################################
> #--------------------------------------------
> #@# Cortical ribbon mask Tue Mar 13 20:04:06 CET 2018
> /usr/local/freesurfer/subjects/AVGmonkeys/mri
>
>  mris_volmask --aseg_name aseg.presurf --label_left_white 2
> --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon

42

...

> --save_ribbon AVGmonkeys
>
> SUBJECTS_DIR is /usr/local/freesurfer/subjects
> loading input data...
> computing distance to left white surface
> computing distance to left pial surface
> computing distance to right white surface
> computing distance to right pial surface
>  hemi masks overlap voxels = 34535
> writing volume
/usr/local/freesurfer/subjects/AVGmonkeys/mri/ribbon.mgz
> ERROR: ribbon has non-zero value at location 0,0,0
> Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12

21:23:04

...

> UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s AVGmonkeys exited with ERRORS at Tue Mar 13
20:26:58 CET 2018
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584 <tel:%2B972%2058%20444%202584>
> E-mail: francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.

harvard.edu>

...

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>


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-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il mailto:francesca.strappini@weizmann.ac.il

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Thanks Doug! Actually talairach.lta looks quite good. However, when I tried to make_average_subject with --xform talairach.lta I got immediately an error:

make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects /usr/local/freesurfer/bin/make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

$Id: make_average_subject,v 1.23.2.1 2016/08/02 21:20:04 greve Exp $ Fri Mar 16 10:20:30 CET 2018 /usr/local/freesurfer/subjects output ddir is /usr/local/freesurfer/subjects uid=1000(francesca) gid=1000(francesca) groups=1000(francesca),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),113(lpadmin),128(sambashare) make_average_surface --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects /usr/local/freesurfer/bin/make_average_surface --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

$Id: make_average_surface,v 1.62 2016/02/16 17:17:20 zkaufman Exp $ Fri Mar 16 10:20:30 CET 2018 /usr/local/freesurfer/subjects/AVGmonkey output ddir is /usr/local/freesurfer/subjects uid=1000(francesca) gid=1000(francesca) groups=1000(francesca),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),113(lpadmin),128(sambashare) ==================== make_average_surface ==================== Fri Mar 16 10:20:30 CET 2018 /usr/local/freesurfer/subjects/AVGmonkey /usr/local/freesurfer/bin/make_average_surface --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta input subjects: MonkeyCelia MonkeyCassis output subject: AVGmonkey mri_add_xform_to_header -c auto /usr/local/freesurfer/subjects/AVGmonkey/mri/mni305.cor.mgz /usr/local/freesurfer/subjects/AVGmonkey/mri/mni305.cor.mgz INFO: extension is mgz

#@# Making lh registration template --------- /usr/local/freesurfer/subjects/AVGmonkey mris_make_template -norot -annot aparc lh sphere.reg MonkeyCelia MonkeyCassis lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject MonkeyCelia (1 of 2) reading spherical surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.inflated.H... curvature mean = -0.074, std = 1.020 computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.sulc... computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.smoothwm...

processing subject MonkeyCassis (2 of 2) reading spherical surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.sphere.reg... curvature mean = -0.041, std = 3.478 curvature mean = -0.056, std = 0.439 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.inflated.H... curvature mean = -0.048, std = 1.029 computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.sulc... computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.smoothwm... writing updated template with 2 subjects to lh.reg.template.tif... curvature mean = 0.038, std = 4.146 curvature mean = -0.062, std = 0.305

#@# Making rh registration template --------- /usr/local/freesurfer/subjects/AVGmonkey mris_make_template -norot -annot aparc rh sphere.reg MonkeyCelia MonkeyCassis rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject MonkeyCelia (1 of 2) reading spherical surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/rh.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/rh.inflated.H... curvature mean = -0.056, std = 0.973 computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/rh.sulc... computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCelia/surf/rh.smoothwm...

processing subject MonkeyCassis (2 of 2) reading spherical surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.sphere.reg... curvature mean = -0.081, std = 3.305 curvature mean = -0.051, std = 0.316 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.inflated.H... curvature mean = -0.059, std = 1.018 computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.sulc... computing parameterization for surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/rh.smoothwm... writing updated template with 2 subjects to rh.reg.template.tif... curvature mean = 0.036, std = 4.168 curvature mean = -0.068, std = 0.371

#@# Making average lh.white surface --------------------- Fri Mar 16 10:20:34 CET 2018 /usr/local/freesurfer/subjects/AVGmonkey mris_make_average_surface -X talairach.lta -i 7 -o white -sdir-out /usr/local/freesurfer/subjects lh white sphere.reg AVGmonkey MonkeyCelia MonkeyCassis using xform talairach.lta... reading vertex positions from white... --------------------------------------------------- hemi = lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = AVGmonkey xform = talairach.lta ---------------------------------------------------

--------------------------------------------------- #@# processing subject 1/2 MonkeyCelia... Reading /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.sphere.reg Read /usr/local/freesurfer/subjects/MonkeyCelia/mri/T1.mgz Surface area: 86.0 cm^2 ERROR: don't know what to do with talairach.lta mris_average_surface failed ERROR: make_average_surface

2018-03-15 23:18 GMT+01:00 Douglas N. Greve dgreve@mgh.harvard.edu:

See if the talairach.lta is any better, eg

cd subject/mri/transforms

tkregister --mov ../nu.mgz --s fsaverage --reg talairach.lta

If so, you can try running make_average_subject with --xform talairach.lta

I've never done this, but it might work :)

On 03/15/2018 01:02 PM, Francesca Strappini wrote:

...

Thank you, Doug! One monkey has a pretty decent registration while the other one does not even appear in the window when I try to manually check the registration with this command line: tkregister --mgz --s MonkeyCelia --fstal --surf orig It looks like if there is no brain.

2018-03-15 16:57 GMT+01:00 Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:

Check the talairach.xfm registration. It is probably way off. It does
not have to be perfect (esp since they are different species), but

the

...

two subjects should have a similar registration


On 03/14/2018 07:27 PM, Francesca Strappini wrote:
> Both average hemispheres look very bad, they don't even look like a
> brain. The two monkey surfaces look reasonable, except for some
> topological defect that I think could be fixed with some manual
> editing. Is there anything I could try?
>
> Thanks a lot
> Francesca
>
> 2018-03-14 23:41 GMT+01:00 Douglas N. Greve
<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>
> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>:
>
>     I don't know what is going on there except that the average
>     surfaces are
>     probably wrong in some way. It looks like it made it all the

way

...

>     through
>     except for that step, so all of the output should be there. How
>     does it
>     look?
>
>
>     On 03/13/2018 05:27 PM, Francesca Strappini wrote:
>     > Dear Experts,
>     >
>     > I'm trying to average two monkey brains. I run this
command line:
>     >
>     >  make_average_subject --subjects MonkeyCelia MonkeyCassis
--out
>     AVGmonkeys
>     >
>     > but it ended with errors.
>     >
>     > I run the recon-all for both monkyes with the option
-notal-check
>     > because I had problems with the Talairach registration. I
don't know
>     > if this could be the cause.
>     >
>     > Thanks a lot
>     > Francesca
>     >
>     > Tue Mar 13 20:04:06 CET 2018
>     > /usr/local/freesurfer/subjects/AVGmonkeys
>     > /usr/local/freesurfer/bin/recon-all
>     > -s AVGmonkeys -cortribbon -aparc2aseg
>     > subjid AVGmonkeys
>     > setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
>     > FREESURFER_HOME /usr/local/freesurfer
>     > Actual FREESURFER_HOME /usr/local/freesurfer
>     > build-stamp.txt:
>     freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>     > Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb
12 21:23:04
>     > UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>     > cputime      unlimited
>     > filesize     unlimited
>     > datasize     unlimited
>     > stacksize    8192 kbytes
>     > coredumpsize 0 kbytes
>     > memoryuse    unlimited
>     > vmemoryuse   unlimited
>     > descriptors  1024
>     > memorylocked 64 kbytes
>     > maxproc      63682
>     > maxlocks     unlimited
>     > maxsignal    63682
>     > maxmessage   819200
>     > maxnice      0
>     > maxrtprio    0
>     > maxrttime    unlimited
>     >
>     >               total        used free shared buff/cache
>     > available
>     > Mem:       16350220     4943572 7520800 278988 3885848
>     > 10739864
>     > Swap:      19528700           0 19528700
>     >
>     > ########################################
>     > program versions used
>     > $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp

$

...

>     > $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20
zkaufman
>     Exp $
>     > mri_convert.bin -all-info
>     > ProgramName: mri_convert.bin ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_convert.c,v
>     1.226
>     > 2016/02/26 16:15:24 mreuter Exp $  User: francesca
Machine: shalimpc
>     > Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     CompilerName: GCC
>     > CompilerVersion: 40400
>     > FLIRT version 5.5
>     > $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
>     > mri_convert.bin --version
>     > stable6
>     > ProgramName: tkregister2_cmdl ProgramArguments: --all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
tkregister2.c,v
>     > 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: francesca
Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > Program nu_correct, built from:
>     > Package MNI N3, version 1.12.0, compiled by nicks@terrier
>     > (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
>     > ProgramName: mri_make_uchar ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mri_make_uchar.c,v 1.4
>     > 2011/03/02 00:04:14 nicks Exp $  User: francesca Machine:
shalimpc
>     > Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_normalize ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_normalize.c,v
>     > 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_watershed ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_watershed.cpp,v
>     > 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: francesca
Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_gcut  ProgramArguments: -all-info
ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14

2011/03/02

...

>     > 00:04:16 nicks Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_segment ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp: Jan 18
>     > 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27
>     22:24:52
>     > zkaufman Exp $  User: francesca  Machine: shalimpc
Platform: Linux
>     > PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     CompilerVersion:
>     > 40400
>     > ProgramName: mri_label2label.bin ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_label2label.c,v
>     > 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_em_register ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_em_register.c,v
>     > 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User: francesca
>     > Machine: shalimpc Platform: Linux PlatformVersion:
>     4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_ca_normalize ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_ca_normalize.c,v
>     > 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_ca_register ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_ca_register.c,v
>     > 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_ca_label ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp: Jan 18
>     > 2017 16:38:58  CVS: $Id: mri_ca_label.c,v 1.113.2.2

2016/10/27

...

>     > 22:25:10 zkaufman Exp $  User: francesca Machine: shalimpc
>     Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_pretess ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_pretess.c,v 1.22
2013/08/30
>     > 18:12:25 mreuter Exp $  User: francesca Machine: shalimpc
>     Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_fill  ProgramArguments: -all-info
ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_fill.c,v 1.119 2011/10/25
>     14:09:58
>     > fischl Exp $  User: francesca  Machine: shalimpc Platform:
Linux
>     > PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_tessellate ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_tessellate.c,v
>     > 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_concatenate_lta.bin ProgramArguments:
-all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp
$  User:
>     > francesca  Machine: shalimpc Platform: Linux PlatformVersion:
>     > 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400
>     > ProgramName: mri_normalize_tp2 ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mri_normalize_tp2.c,v
>     > 1.8 2011/03/02 00:04:23 nicks Exp $  User: francesca

Machine:

...

>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_smooth ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30
2014/01/21
>     > 18:48:21 fischl Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_inflate ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45
2016/01/20
>     > 23:42:15 greve Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_curvature ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mris_curvature.c,v
>     > 1.31 2011/03/02 00:04:30 nicks Exp $ User: francesca

Machine:

...

>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_sphere ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mris_sphere.c,v 1.61
2016/01/20
>     > 23:42:15 greve Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_fix_topology ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_fix_topology.c,v
>     > 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc  Platform: Linux PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_topo_fixer ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_topo_fixer.cpp,v
>     > 1.29 2011/03/02 00:04:34 nicks Exp $ User: francesca

Machine:

...

>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_ca_label ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_ca_label.c,v 1.37
>     > 2014/02/04 17:46:42 fischl Exp $  User: francesca Machine:
shalimpc
>     > Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_euler_number ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_euler_number.c,v
>     > 1.10 2013/01/14 22:39:14 greve Exp $ User: francesca

Machine:

...

>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_make_surfaces ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_make_surfaces.c,v
>     > 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc  Platform: Linux PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_register ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_register.c,v 1.63
>     > 2016/01/20 23:43:04 greve Exp $  User: francesca Machine:
shalimpc
>     > Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_volmask ProgramArguments: --all-info
>     > ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mris_volmask.cpp,v
>     > 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_anatomical_stats ProgramArguments:

-all-info

...

>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve
Exp $
>     User:
>     > francesca  Machine: shalimpc  Platform: Linux

PlatformVersion:

...

>     > 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
>     > ProgramName: mrisp_paint ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mrisp_paint.c,v 1.12
2016/03/22
>     > 14:47:57 fischl Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_curvature_stats ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks
Exp $  User:
>     > francesca  Machine: shalimpc Platform: Linux PlatformVersion:
>     > 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400
>     > ProgramName: mris_calc  ProgramArguments: -all-info
ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mris_calc.c,v 1.54.2.1
2016/09/27
>     > 18:51:28 greve Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17
greve Exp $
>     >
>     > ProgramName: mri_robust_register.bin ProgramArguments:
-all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve
Exp $
>     User:
>     > francesca  Machine: shalimpc  Platform: Linux

PlatformVersion:

...

>     > 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
>     > $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08
mreuter
>     Exp $
>     >
>     > ProgramName: mri_robust_template ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter
Exp $
>     > User: francesca  Machine: shalimpc Platform: Linux
>     PlatformVersion:
>     > 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
>     > ProgramName: mri_and  ProgramArguments: -all-info
ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_and.c,v 1.4 2011/03/02
00:04:13
>     > nicks Exp $  User: francesca  Machine: shalimpc Platform:
Linux
>     > PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_or  ProgramArguments: -all-info
ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_or.c,v 1.5 2013/03/20
15:03:29
>     > lzollei Exp $  User: francesca  Machine: shalimpc
Platform: Linux
>     > PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_fuse_segmentations ProgramArguments:
-all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks
Exp $
>     User:
>     > francesca  Machine: shalimpc  Platform: Linux

PlatformVersion:

...

>     > 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
>     > ProgramName: mri_segstats ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_segstats.c,v 1.121
2016/05/31
>     > 17:27:11 greve Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_relabel_hypointensities ProgramArguments:
>     -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10

nicks

...

>     Exp $
>     > User: francesca  Machine: shalimpc Platform: Linux
>     PlatformVersion:
>     > 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
>     > #######################################
>     > GCADIR /usr/local/freesurfer/average
>     > GCA RB_all_2016-05-10.vc700.gca
>     > GCASkull RB_all_withskull_2016-05-10.vc700.gca
>     > AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
>     > GCSDIR /usr/local/freesurfer/average
>     > GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
>     > #######################################
>     > #--------------------------------------------
>     > #@# Cortical ribbon mask Tue Mar 13 20:04:06 CET 2018
>     > /usr/local/freesurfer/subjects/AVGmonkeys/mri
>     >
>     >  mris_volmask --aseg_name aseg.presurf --label_left_white 2
>     > --label_left_ribbon 3 --label_right_white 41
--label_right_ribbon 42
>     > --save_ribbon AVGmonkeys
>     >
>     > SUBJECTS_DIR is /usr/local/freesurfer/subjects
>     > loading input data...
>     > computing distance to left white surface
>     > computing distance to left pial surface
>     > computing distance to right white surface
>     > computing distance to right pial surface
>     >  hemi masks overlap voxels = 34535
>     > writing volume
>     /usr/local/freesurfer/subjects/AVGmonkeys/mri/ribbon.mgz
>     > ERROR: ribbon has non-zero value at location 0,0,0
>     > Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb
12 21:23:04
>     > UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>     >
>     > recon-all -s AVGmonkeys exited with ERRORS at Tue Mar 13
>     20:26:58 CET 2018
>     >
>     > To report a problem, see
>     > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
>     >
>     >
>     > --
>     > Francesca Strappini, Ph.D.
>     > Neurobiology Department
>     > Weizmann Institute of Science
>     > 234 Herzl Street, Rehovot 7610001 Israel
>     > Tel.: +972 58 444 2584 <tel:%2B972%2058%20444%202584>
<tel:%2B972%2058%20444%202584>
>     > E-mail: francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>
>     <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>>
>     > <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>
>     <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>>>
>     >
>     >
>     > _______________________________________________
>     > Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     >
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>     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>
>     _______________________________________________
>     Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>
>
>     The information in this e-mail is intended only for the
person to
>     whom it is
>     addressed. If you believe this e-mail was sent to you in
error and
>     the e-mail
>     contains patient information, please contact the Partners
>     Compliance HelpLine at
> http://www.partners.org/complianceline
<http://www.partners.org/complianceline>
>     <http://www.partners.org/complianceline
<http://www.partners.org/complianceline>> . If the e-mail was sent
>     to you in error
>     but does not contain patient information, please contact the
>     sender and properly
>     dispose of the e-mail.
>
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>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584 <tel:%2B972%2058%20444%202584>
> E-mail: francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>>
>
>
> _______________________________________________
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.

harvard.edu>

...

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il mailto:francesca.strappini@weizmann.ac.il

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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That worked! Thanks a lot :) I suppose that I could improve the appearance with some further manual editing of the surfaces.

Best Francesca

2018-03-16 16:17 GMT+01:00 Douglas Greve dgreve@mgh.harvard.edu:

Try this:

1. make a back up of the talairach.xfm

cp talairach.xfm bak.talarach.xfm

2. Convert the lta to an xfm:

tkregister --mov ../orig.mgz --lta talairach.lta --reg deleteme.reg.dat --xfmout talairach.xfm --s fsaverage --surfs --noedit

3. rerun make_average_subject

On 3/16/18 5:24 AM, Francesca Strappini wrote:

Thanks Doug! Actually talairach.lta looks quite good. However, when I tried to make_average_subject with --xform talairach.lta I got immediately an error:

make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects /usr/local/freesurfer/bin/make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

$Id: make_average_subject,v 1.23.2.1 2016/08/02 21:20:04 greve Exp $ Fri Mar 16 10:20:30 CET 2018 /usr/local/freesurfer/subjects output ddir is /usr/local/freesurfer/subjects uid=1000(francesca) gid=1000(francesca) groups=1000(francesca),4(adm), 24(cdrom),27(sudo),30(dip),46(plugdev),113(lpadmin),128(sambashare) make_average_surface --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects /usr/local/freesurfer/bin/make_average_surface --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta

$Id: make_average_surface,v 1.62 2016/02/16 17:17:20 zkaufman Exp $ Fri Mar 16 10:20:30 CET 2018 /usr/local/freesurfer/subjects/AVGmonkey output ddir is /usr/local/freesurfer/subjects uid=1000(francesca) gid=1000(francesca) groups=1000(francesca),4(adm), 24(cdrom),27(sudo),30(dip),46(plugdev),113(lpadmin),128(sambashare) ==================== make_average_surface ==================== Fri Mar 16 10:20:30 CET 2018 /usr/local/freesurfer/subjects/AVGmonkey /usr/local/freesurfer/bin/make_average_surface --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta input subjects: MonkeyCelia MonkeyCassis output subject: AVGmonkey mri_add_xform_to_header -c auto /usr/local/freesurfer/ subjects/AVGmonkey/mri/mni305.cor.mgz /usr/local/freesurfer/ subjects/AVGmonkey/mri/mni305.cor.mgz INFO: extension is mgz

#@# Making lh registration template --------- /usr/local/freesurfer/subjects/AVGmonkey mris_make_template -norot -annot aparc lh sphere.reg MonkeyCelia MonkeyCassis lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject MonkeyCelia (1 of 2) reading spherical surface /usr/local/freesurfer/ subjects/MonkeyCelia/surf/lh.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/ greve/fsdev.build/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCelia/surf/lh.inflated.H... curvature mean = -0.074, std = 1.020 computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCelia/surf/lh.sulc... computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCelia/surf/lh.smoothwm...

processing subject MonkeyCassis (2 of 2) reading spherical surface /usr/local/freesurfer/ subjects/MonkeyCassis/surf/lh.sphere.reg... curvature mean = -0.041, std = 3.478 curvature mean = -0.056, std = 0.439 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/ greve/fsdev.build/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCassis/surf/lh.inflated.H... curvature mean = -0.048, std = 1.029 computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCassis/surf/lh.sulc... computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCassis/surf/lh.smoothwm... writing updated template with 2 subjects to lh.reg.template.tif... curvature mean = 0.038, std = 4.146 curvature mean = -0.062, std = 0.305

#@# Making rh registration template --------- /usr/local/freesurfer/subjects/AVGmonkey mris_make_template -norot -annot aparc rh sphere.reg MonkeyCelia MonkeyCassis rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject MonkeyCelia (1 of 2) reading spherical surface /usr/local/freesurfer/ subjects/MonkeyCelia/surf/rh.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/ greve/fsdev.build/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCelia/surf/rh.inflated.H... curvature mean = -0.056, std = 0.973 computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCelia/surf/rh.sulc... computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCelia/surf/rh.smoothwm...

processing subject MonkeyCassis (2 of 2) reading spherical surface /usr/local/freesurfer/ subjects/MonkeyCassis/surf/rh.sphere.reg... curvature mean = -0.081, std = 3.305 curvature mean = -0.051, std = 0.316 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/ greve/fsdev.build/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCassis/surf/rh.inflated.H... curvature mean = -0.059, std = 1.018 computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCassis/surf/rh.sulc... computing parameterization for surface /usr/local/freesurfer/ subjects/MonkeyCassis/surf/rh.smoothwm... writing updated template with 2 subjects to rh.reg.template.tif... curvature mean = 0.036, std = 4.168 curvature mean = -0.068, std = 0.371

#@# Making average lh.white surface --------------------- Fri Mar 16 10:20:34 CET 2018 /usr/local/freesurfer/subjects/AVGmonkey mris_make_average_surface -X talairach.lta -i 7 -o white -sdir-out /usr/local/freesurfer/subjects lh white sphere.reg AVGmonkey MonkeyCelia MonkeyCassis using xform talairach.lta... reading vertex positions from white...

---

hemi = lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = AVGmonkey xform = talairach.lta

---

---

#@# processing subject 1/2 MonkeyCelia... Reading /usr/local/freesurfer/subjects/MonkeyCelia/surf/lh.sphere.reg Read /usr/local/freesurfer/subjects/MonkeyCelia/mri/T1.mgz Surface area: 86.0 cm^2 ERROR: don't know what to do with talairach.lta mris_average_surface failed ERROR: make_average_surface

2018-03-15 23:18 GMT+01:00 Douglas N. Greve dgreve@mgh.harvard.edu:

...

See if the talairach.lta is any better, eg

cd subject/mri/transforms

tkregister --mov ../nu.mgz --s fsaverage --reg talairach.lta

If so, you can try running make_average_subject with --xform talairach.lta

I've never done this, but it might work :)

On 03/15/2018 01:02 PM, Francesca Strappini wrote:

...

Thank you, Doug! One monkey has a pretty decent registration while the other one does not even appear in the window when I try to manually check the registration with this command line: tkregister --mgz --s MonkeyCelia --fstal --surf orig It looks like if there is no brain.

2018-03-15 16:57 GMT+01:00 Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:

Check the talairach.xfm registration. It is probably way off. It

does

...

not have to be perfect (esp since they are different species), but

the

...

two subjects should have a similar registration


On 03/14/2018 07:27 PM, Francesca Strappini wrote:
> Both average hemispheres look very bad, they don't even look like

a

...

> brain. The two monkey surfaces look reasonable, except for some
> topological defect that I think could be fixed with some manual
> editing. Is there anything I could try?
>
> Thanks a lot
> Francesca
>
> 2018-03-14 23:41 GMT+01:00 Douglas N. Greve
<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>
> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>>:
>
>     I don't know what is going on there except that the average
>     surfaces are
>     probably wrong in some way. It looks like it made it all the

way

...

>     through
>     except for that step, so all of the output should be there.

How

...

>     does it
>     look?
>
>
>     On 03/13/2018 05:27 PM, Francesca Strappini wrote:
>     > Dear Experts,
>     >
>     > I'm trying to average two monkey brains. I run this
command line:
>     >
>     >  make_average_subject --subjects MonkeyCelia MonkeyCassis
--out
>     AVGmonkeys
>     >
>     > but it ended with errors.
>     >
>     > I run the recon-all for both monkyes with the option
-notal-check
>     > because I had problems with the Talairach registration. I
don't know
>     > if this could be the cause.
>     >
>     > Thanks a lot
>     > Francesca
>     >
>     > Tue Mar 13 20:04:06 CET 2018
>     > /usr/local/freesurfer/subjects/AVGmonkeys
>     > /usr/local/freesurfer/bin/recon-all
>     > -s AVGmonkeys -cortribbon -aparc2aseg
>     > subjid AVGmonkeys
>     > setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
>     > FREESURFER_HOME /usr/local/freesurfer
>     > Actual FREESURFER_HOME /usr/local/freesurfer
>     > build-stamp.txt:
>     freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>     > Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb
12 21:23:04
>     > UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>     > cputime      unlimited
>     > filesize     unlimited
>     > datasize     unlimited
>     > stacksize    8192 kbytes
>     > coredumpsize 0 kbytes
>     > memoryuse    unlimited
>     > vmemoryuse   unlimited
>     > descriptors  1024
>     > memorylocked 64 kbytes
>     > maxproc      63682
>     > maxlocks     unlimited
>     > maxsignal    63682
>     > maxmessage   819200
>     > maxnice      0
>     > maxrtprio    0
>     > maxrttime    unlimited
>     >
>     >               total        used free shared buff/cache
>     > available
>     > Mem:       16350220     4943572 7520800 278988 3885848
>     > 10739864
>     > Swap:      19528700           0 19528700
>     >
>     > ########################################
>     > program versions used
>     > $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman

Exp $

...

>     > $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20
zkaufman
>     Exp $
>     > mri_convert.bin -all-info
>     > ProgramName: mri_convert.bin ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_convert.c,v
>     1.226
>     > 2016/02/26 16:15:24 mreuter Exp $  User: francesca
Machine: shalimpc
>     > Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     CompilerName: GCC
>     > CompilerVersion: 40400
>     > FLIRT version 5.5
>     > $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
>     > mri_convert.bin --version
>     > stable6
>     > ProgramName: tkregister2_cmdl ProgramArguments: --all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
tkregister2.c,v
>     > 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: francesca
Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > Program nu_correct, built from:
>     > Package MNI N3, version 1.12.0, compiled by nicks@terrier
>     > (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
>     > ProgramName: mri_make_uchar ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mri_make_uchar.c,v 1.4
>     > 2011/03/02 00:04:14 nicks Exp $  User: francesca Machine:
shalimpc
>     > Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_normalize ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp:

2018/03/13-19:04:06-GMT

...

>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_normalize.c,v
>     > 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_watershed ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_watershed.cpp,v
>     > 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: francesca
Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_gcut  ProgramArguments: -all-info
ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14

2011/03/02

...

>     > 00:04:16 nicks Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_segment ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp: Jan 18
>     > 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27
>     22:24:52
>     > zkaufman Exp $  User: francesca  Machine: shalimpc
Platform: Linux
>     > PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     CompilerVersion:
>     > 40400
>     > ProgramName: mri_label2label.bin ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp:

2018/03/13-19:04:06-GMT

...

>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_label2label.c,v
>     > 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_em_register ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp:

2018/03/13-19:04:06-GMT

...

>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_em_register.c,v
>     > 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User:

francesca

...

>     > Machine: shalimpc Platform: Linux PlatformVersion:
>     4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_ca_normalize ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp:

2018/03/13-19:04:06-GMT

...

>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_ca_normalize.c,v
>     > 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_ca_register ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp:

2018/03/13-19:04:06-GMT

...

>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_ca_register.c,v
>     > 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_ca_label ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name:  $  TimeStamp: 2018/03/13-19:04:06-GMT
BuildTimeStamp: Jan 18
>     > 2017 16:38:58  CVS: $Id: mri_ca_label.c,v 1.113.2.2

2016/10/27

...

>     > 22:25:10 zkaufman Exp $  User: francesca Machine: shalimpc
>     Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_pretess ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_pretess.c,v 1.22
2013/08/30
>     > 18:12:25 mreuter Exp $  User: francesca Machine: shalimpc
>     Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_fill  ProgramArguments: -all-info
ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_fill.c,v 1.119

2011/10/25

...

>     14:09:58
>     > fischl Exp $  User: francesca  Machine: shalimpc Platform:
Linux
>     > PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_tessellate ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp:

2018/03/13-19:04:06-GMT

...

>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mri_tessellate.c,v
>     > 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mri_concatenate_lta.bin ProgramArguments:
-all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp
$  User:
>     > francesca  Machine: shalimpc Platform: Linux

PlatformVersion:

...

>     > 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400
>     > ProgramName: mri_normalize_tp2 ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mri_normalize_tp2.c,v
>     > 1.8 2011/03/02 00:04:23 nicks Exp $  User: francesca

Machine:

...

>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_smooth ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30
2014/01/21
>     > 18:48:21 fischl Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_inflate ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45
2016/01/20
>     > 23:42:15 greve Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_curvature ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mris_curvature.c,v
>     > 1.31 2011/03/02 00:04:30 nicks Exp $ User: francesca

Machine:

...

>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_sphere ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mris_sphere.c,v 1.61
2016/01/20
>     > 23:42:15 greve Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_fix_topology ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp:

2018/03/13-19:04:06-GMT

...

>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_fix_topology.c,v
>     > 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc  Platform: Linux PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_topo_fixer ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_topo_fixer.cpp,v
>     > 1.29 2011/03/02 00:04:34 nicks Exp $ User: francesca

Machine:

...

>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_ca_label ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_ca_label.c,v 1.37
>     > 2014/02/04 17:46:42 fischl Exp $  User: francesca Machine:
shalimpc
>     > Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_euler_number ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_euler_number.c,v
>     > 1.10 2013/01/14 22:39:14 greve Exp $ User: francesca

Machine:

...

>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_make_surfaces ProgramArguments: -all-info
>     > ProgramVersion: $Name:  $  TimeStamp:

2018/03/13-19:04:06-GMT

...

>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_make_surfaces.c,v
>     > 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $  User:

francesca

...

>     Machine:
>     > shalimpc  Platform: Linux PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_register ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     mris_register.c,v 1.63
>     > 2016/01/20 23:43:04 greve Exp $  User: francesca Machine:
shalimpc
>     > Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_volmask ProgramArguments: --all-info
>     > ProgramVersion: $Name:  $  TimeStamp:

2018/03/13-19:04:06-GMT

...

>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
mris_volmask.cpp,v
>     > 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $  User: francesca
>     Machine:
>     > shalimpc Platform: Linux  PlatformVersion: 4.4.0-116-generic
>     > CompilerName: GCC  CompilerVersion: 40400
>     > ProgramName: mris_anatomical_stats ProgramArguments:

-all-info

...

>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve
Exp $
>     User:
>     > francesca  Machine: shalimpc  Platform: Linux

PlatformVersion:

...

>     > 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
>     > ProgramName: mrisp_paint ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mrisp_paint.c,v 1.12
2016/03/22
>     > 14:47:57 fischl Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mris_curvature_stats ProgramArguments:

-all-info

...

>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks
Exp $  User:
>     > francesca  Machine: shalimpc Platform: Linux

PlatformVersion:

...

>     > 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400
>     > ProgramName: mris_calc  ProgramArguments: -all-info
ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mris_calc.c,v 1.54.2.1
2016/09/27
>     > 18:51:28 greve Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17
greve Exp $
>     >
>     > ProgramName: mri_robust_register.bin ProgramArguments:
-all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve
Exp $
>     User:
>     > francesca  Machine: shalimpc  Platform: Linux

PlatformVersion:

...

>     > 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
>     > $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08
mreuter
>     Exp $
>     >
>     > ProgramName: mri_robust_template ProgramArguments: -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter
Exp $
>     > User: francesca  Machine: shalimpc Platform: Linux
>     PlatformVersion:
>     > 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
>     > ProgramName: mri_and  ProgramArguments: -all-info
ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_and.c,v 1.4 2011/03/02
00:04:13
>     > nicks Exp $  User: francesca  Machine: shalimpc Platform:
Linux
>     > PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_or  ProgramArguments: -all-info
ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_or.c,v 1.5 2013/03/20
15:03:29
>     > lzollei Exp $  User: francesca  Machine: shalimpc
Platform: Linux
>     > PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_fuse_segmentations ProgramArguments:
-all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks
Exp $
>     User:
>     > francesca  Machine: shalimpc  Platform: Linux

PlatformVersion:

...

>     > 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
>     > ProgramName: mri_segstats ProgramArguments: -all-info
>     ProgramVersion:
>     > $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-GMT
>     BuildTimeStamp:
>     > Jan 18 2017 16:38:58  CVS: $Id: mri_segstats.c,v 1.121
2016/05/31
>     > 17:27:11 greve Exp $  User: francesca Machine: shalimpc
Platform:
>     > Linux  PlatformVersion: 4.4.0-116-generic CompilerName: GCC
>     > CompilerVersion: 40400
>     > ProgramName: mri_relabel_hypointensities ProgramArguments:
>     -all-info
>     > ProgramVersion: $Name: stable6 $ TimeStamp:
>     2018/03/13-19:04:06-GMT
>     > BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id:
>     > mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10

nicks

...

>     Exp $
>     > User: francesca  Machine: shalimpc Platform: Linux
>     PlatformVersion:
>     > 4.4.0-116-generic  CompilerName: GCC CompilerVersion: 40400
>     > #######################################
>     > GCADIR /usr/local/freesurfer/average
>     > GCA RB_all_2016-05-10.vc700.gca
>     > GCASkull RB_all_withskull_2016-05-10.vc700.gca
>     > AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
>     > GCSDIR /usr/local/freesurfer/average
>     > GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
>     > #######################################
>     > #--------------------------------------------
>     > #@# Cortical ribbon mask Tue Mar 13 20:04:06 CET 2018
>     > /usr/local/freesurfer/subjects/AVGmonkeys/mri
>     >
>     >  mris_volmask --aseg_name aseg.presurf --label_left_white 2
>     > --label_left_ribbon 3 --label_right_white 41
--label_right_ribbon 42
>     > --save_ribbon AVGmonkeys
>     >
>     > SUBJECTS_DIR is /usr/local/freesurfer/subjects
>     > loading input data...
>     > computing distance to left white surface
>     > computing distance to left pial surface
>     > computing distance to right white surface
>     > computing distance to right pial surface
>     >  hemi masks overlap voxels = 34535
>     > writing volume
>     /usr/local/freesurfer/subjects/AVGmonkeys/mri/ribbon.mgz
>     > ERROR: ribbon has non-zero value at location 0,0,0
>     > Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb
12 21:23:04
>     > UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>     >
>     > recon-all -s AVGmonkeys exited with ERRORS at Tue Mar 13
>     20:26:58 CET 2018
>     >
>     > To report a problem, see
>     > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
>     >
>     >
>     > --
>     > Francesca Strappini, Ph.D.
>     > Neurobiology Department
>     > Weizmann Institute of Science
>     > 234 Herzl Street, Rehovot 7610001 Israel
>     > Tel.: +972 58 444 2584 <%2B972%2058%20444%202584>

tel:%2B972%2058%20444%202584 <%2B972%2058%20444%202584>

...

<tel:%2B972%2058%20444%202584> <%2B972%2058%20444%202584>
>     > E-mail: francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>
>     <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>>
>     > <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>
>     <mailto:francesca.strappini@weizmann.ac.il
<mailto:francesca.strappini@weizmann.ac.il>>>
>     >
>     >
>     > _______________________________________________
>     > Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>
>     _______________________________________________
>     Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>
>
>     The information in this e-mail is intended only for the
person to
>     whom it is
>     addressed. If you believe this e-mail was sent to you in
error and
>     the e-mail
>     contains patient information, please contact the Partners
>     Compliance HelpLine at
> http://www.partners.org/complianceline
<http://www.partners.org/complianceline>
>     <http://www.partners.org/complianceline
<http://www.partners.org/complianceline>> . If the e-mail was sent
>     to you in error
>     but does not contain patient information, please contact the
>     sender and properly
>     dispose of the e-mail.
>
>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584 <%2B972%2058%20444%202584>

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> E-mail: francesca.strappini@weizmann.ac.il
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-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 <%2B972%2058%20444%202584> E-mail: francesca.strappini@weizmann.ac.il mailto:francesca.strappini@weizmann.ac.il

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-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 <+972%2058-444-2584> E-mail: francesca.strappini@weizmann.ac.il

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